Rethroned
by Cheesus333
Summary: The fate of all life in the galaxy is once again in Shepard's hands as an old enemy returns with a bitter vengeance.
1. Chapter 1

Shepard slipped the fresh heat clip into the gun, and chambered the next round. He peered down the scope.

"Seven hostiles – three mechs, four mercs," he spoke in hushed tones to Thane, who was perched beside him. "Do your stuff, Thane. No mercy."

The Drell slipped down over the ledge, and landed silently. He withdrew his sidearm, and charged up a biotic with his free hand. The mercs – Blue Suns, Shepard observed – were facing the other way, but Thane soon triggered the mech's sensors.

Not that it mattered.

Three rounds, fired in quick succession, were unloaded from Shepard's rifle. Each one found its target easily enough. One, two, three mech viewscreens exploded, scattering shards of weak alloy about the ground. The combat droids collapsed as the four mercs began to turn. Two were lifted into the air by Thane, who then clenched a fist and set them soaring off the bridge. The other two scrambled for their assault, rifles, but never found them. A Krogan battlecry was the last thing they heard as Grunt pounced from behind, and rammed their faces into the steel floor. Thane finished the job with a round to each, and with a flourish, pocketed his weapon.

"Nice work," spoke Shepard over the comm network, "meet you down there in two."

The Commander hooked a strong metal cable to a peg he had embedded in the lip of the cliff, and the two metals instantly welded themselves together. He fastened the cable to his belt, and began to rapel down the face of the rock.

"Shepard, something troubles me," said the Drell, mandibles clicking with suspicion.

"What's the problem?"

"These mercs," he said, lifting one of them from the ground. Thane rolled the corpse over, and indicated his face. It was Batarian, but only just. "They're wrong."

"What the fuck..." Shepard began, inspecting the warped features of the mutated Batarian. The humanoid's eyes were scattered about its face, and it seemed to have one too many. Its mouth was _filled_ with teeth, all jutting out of gums at every angle but the right one.

"What's your diagnosis?" Shepard asked, replacing the corpse beside his partner. Grunt suddenly chipped in.

"I remember this. The early Krogan clones got this sometimes. A little outside contamination in the gene replication could scramble things up... like this."

"You thinking sabotage?" Shepard asked.

"I'm thinking so." Came the gruff reply from his Krogan companion.

"Then it looks like we've got more than one operation to shut down at this base." Shepard rose. "Keep moving, and stay quiet. I'd like to avoid an alarm for as long as we can."

The squad moved through the base silently, assassinating guards and patrols where necessary. Soon, cloning pods came into view: man-sized test tubes for fast-grown soldiers. Each pod had a small screen, and every one was flashing red. Scarlet letters brightened and dimmed on each screen, all reading the same thing.

"CONTAMINATED"

"They're all warped, Shepard," spoke Thane from behind the Commander. "Every one. I don't think we're looking for a _single_ saboteur." Shepard nodded.

"Let's keep going. We'll find out as much as we can, then we'll shut this place down." He looked at the rows of cloning pods. "Explosively, if necessary." Grunt smirked.

The deeper they penetrated the base, the more pods began to show themselves. With a dawning horror, Shepard realised they could open at any second.

"Shepard, over here!" Barked Grunt, pointing at a door set into the rock. The sign above it read "HIVE." They moved to the door.

"If my guess is right, this will be where the majority are stocked. That means guards, and _that_ means trouble. Grunt, set to explosive rounds. Thane, cover us." Shepard drew his Eviscerator shotgun from the back of his waist. "Let's finish these bastards off."

Shepard tapped a button on the doorframe, and the heavy slab of metal began to rise slowly. Suddenly, sirens rang, and a monotonous, automated voice filled the complex.

"WARNING! Intruders at the Hive. Security dispatched."

"Company, Shepard," said the Drell to his left as a concussive shot hit a dent in the slowly ascending door right next to his head. Shepard turned quickly, shotgun raised, and scanned for cover.

"Grunt, behind that crate! Thane, get behind that clone pod!" He barked, sliding along the metal floor to a column stretching from roof to rock. He peered from cover, and in two blasts from the barrel of the Eviscerator managed to shut down two mechs. Four more remained, and these were soon destroyed by Thane's biotics and Grunt's own powerful shotgun. Sweat trickled down Shepard's forehead as he realised the door still wasn't high enough to even roll under, and reinforcements were being sent in the dozens. For every mech that blew apart, two clones stepped into the pile of components, firing madly at the squad.

"Thane, watch that pod!" Cried Shepard, but the noise was too much; Thane was taken completely by surprise as the pod slid open, and deployed a clone, fully dressed in battle armour. The clone yanked the gun from Thane's startled hands, and swung it at the Drell's head. Thane collapsed instantly, groaning once. Shepard checked the door again.

"Grunt, get through that door _now_, and give me covering fire!" The Commander charged at the clone, and seized Thane's rifle from its own hands, which were still dripping with nutrient goo from the pod. Imbuing his free hand with a hefty charge of biotic power, he punched the clone squarely in the chest, and sent him flying back into the ranks of his disfigured brethren.

Bullets whizzed overhead, whistling in his ear as each poorly aimed shard flew past. Shepard grabbed the incapacitated Drell beneath his arms, and dragged him quickly over to the door. Kicking the unconcsious Thane through the yawning mouth of the Hive, Shepard quickly rolled under himself, and shot the control panel on the other side. The door suddenly stopped rising, and – free of its suspension – fell, with a deafening crash, to the ground.

"Now," Shepard said as he stood, wiping away blood and sweat from his visage, "what do we have here?"


	2. Chapter 2

The Salarian, perched over rows and rows of keyboards, stopped his hectic tapping when he heard the pandemonium outside. He was stood on a circular platform, which ringed around an immense glass pole, stretching right from the edge of the cylindrical cavern to the floor, hundreds of feet below. Inside the glass pole, a beam of light was sustained from end to end, pulsing with the synchronised heartbeat of every clone in and out of the complex. The platform itself was only a few meters in diameter, and from the edge of that to the cavern wall was a hollow abyss, with an ominous white light radiating from the bottom. The wall of the chamber was stocked to its maximum capacity with clone pods, and large mechanical arms suspended from the roof served to move them about the chamber, delivering them to various tunnels leading out to the rest of the subterranean lab.

Two paths stretched from the platform, slanting upwards a little to the wall. These were positioned opposite from one another.

When the Salarian noticed the intruders, he quietly but hastily began to pack up his documents into a satchel, and locked the computer at which he previously worked. Then, he began to sneak away, ascending the path opposite Shepard's squad.

"Commander, there's someone over there." The Salarian heard the voice echo from across the span, but kept moving, a little faster now.

"Salarian, if you don't stop, I _will_ stop you." This voice was different. Gruff. Deep. Unmistakably Krogan.

"Shit," the Salarian breathed, realising there was certainly at least one rifle aimed his way at that moment. The scientist turned, and paced back to the platform. He met the squad there.

"What are all these machines?" Spoke their leader, a human. His battle armour was a deep black, with a crimson trim. 'N7' was emblazoned proudly over his chest, to the left. The Salarian sighed. His game was up, and the Blue Suns didn't pay him enough for secrecy under interrogation.

"They control the pods, mainly, but also the mechanical arms. From here, you can send the clones anywhere in the facility, a hundred clones per one arm.

Shepard looked around. The arms seemed very busy: he watched one stop before a row of a hundred pods, and each one opened. Clones stepped onto a narrow platform, apparently unaffected by fear or vertigo, and stood still, waiting for an assignment to be beamed into their heads. The arm then carried its livestock to a tunnel in the wall, and disappeared some way into its inky shadows, only to return free of its load.

"What's wrong with the clones? Why are they all disfigured that way?" Asked a pale-green Drell to the human's left. The Drell wore a thigh-length coat, collar raised to jaw level, and seemed to be eyeing the room as he spoke. His attention to his surroundings suggested military training: his eye for detail suggested more. Assassin, maybe?

"That was my idea. A little element of psychological warfare." Answered the Salarian, increasingly anxious of the silver-white-clad Krogan and his unnecessarily large shotgun. The Krogan was a burnt orange, with shockingly pale eyes – the Salarian's experience in this area led him to believe this Krogan was a tube-bred himself. In an environment like this, that only made him more dangerous.

"Psychological warfare? How do you mean?" The human asked.

"What's scarier than a battalion of armed soldiers coming your way?" Said the Salarian geneticist, leaving the team to fill in the gap.

"A battalion of armed freaks."

"Exactly."

"We can't let this continue. You understand that," said the human, emotionless. He spoke with the manner of a man who was used to shutting down large-scale operations, and it occurred to the Salarian that this infiltration was probably a blue milk run to the veteran Commander.

"I know." The Salarian replied. "Thing is, I don't intend to die for the Blue Suns. So if it's all the same to you, I'd like to leave before whatever you have planned for this facility begins."

"Bullshit," the Krogan snorted, "we let him leave and he either shoots us in the back, or leaves and starts again elsewhere. We only have his word that he's not the mastermind of this whole thing."

"I disagree, Commander," said the Drell, "if this Salarian were really in charge, he would have been much better protected.

"How the hell should you know?" The Krogan barked roughly.

"I was an assassin for most of my life. I know a VIP when I see one, and this scientist is not one." Replied the Drell, confirming the Salarian's assumptions.

"Calm down you two," the human Commander interjected, evidently the master of the situation. "We let him walk. Any funny business, Grunt puts a round up his ass. That sound fair, Salarian?"

The scientist nodded, silent now. However, deep inside his mind, funny business was exactly what he had planned.

"You're a tank-bred, aren't you Krogan?" Said the Salarian confidently.

"I don't discuss it with people I intend to kill. That's you." Grunt, as his name seemed to be, was rough and frank. The archetypical Krogan, the scientist suspected. The quintessential best of his kind. The Salarian vaguely remembered reading about some warlord, O'Keere, he thought, working towards that aim. So the creature before him was a synth... then that meant...

"Failsafe protocol X113." The Salarian spoke sharply. As expected, the Krogan stopped completely.

Grunt dropped his shotgun, then fell to his knees. He began gasping manically, and it didn't take long for the human and his Drell companion to realise he was having a heart attack.

"What the _hell_ did you do to Grunt?" Barked the Commander, pistol raised to the Salarian's face in a fraction of a second. But the scientist had thought this through – his plan was in place.

However, the assassin's reflexes were not a factor he had considered. Before he had a moment to discharge a round from his secretly-withdrawn Carnifex handgun, a lime, humanoid fist had sent his head spiralling. The Salarian fell to the side, weapon cast over the precipice and into the abyss.

"Well crap. I thought I'd gotten away with it then."

"Tell me how to save Grunt's life, and you just might." The human said, sidearm still aimed squarely in the Salarian's face. _No better way then to break bad news than to do it frankly, _thought the panicking scientist.

"You can't. The euthanasia protocols are irreversible, and very permanent. Once he's started dying, he's going to die." The human leaned in close, and whispered gently.

"Then what kind of fucking good are you?"

With a movement so fast no-one could have seen it coming, the Commander twisted on his heel and full-on kicked the Salarian in the chest. The creature's thin, frail figure was light and didn't resist this sudden change in momentum very well: the geneticist was sent backwards over the edge, screaming into eternity and the oblivion he was falling towards.

"Shepard," Thane spoke hurriedly, "we need to stabilise him fast."

"Yeah," the Commander replied, replacing his handgun, "do you have a revival kit, or something like that?"

"No, but... the Normandy's medical wing might." Shepard nodded.

"Joker! EDI!" The Commander yelled into a mouthpiece in his armour, "I need an evac, now!"

"Aye aye, Commander. Shuttle inbound."  
"No, Joker, that won't do. Position the ship over the facility. I have an idea."

"Is this a 'raiding the Citadel with three men and a few guns between you' good idea, or a 'land the ship atop and exploding volcano to save one Asari' good idea?"

"It's a 'save my ass or I'll break your friggin' neck' good idea, Lieutenant, and I'd like it if you _went along with it._"

"Message received, Commander, we're on our way."

"That's more like it." Shepard cut the comms channel.

"What's this idea, Commander?" Asked Thane, lifting the Krogan to his dying feet.

"Not a clue. You got any?"


	3. Chapter 3

Commander Shepard did a lot of things in his line of work. He killed tyrants and criminals indiscriminately. He rescued hostages and prisoners from impossible situations. He saved entire galaxies in mere days with less than a room full of people to help.

Improvising had become something of a talent for him.

"Thane, you think you can work those arm controls?"

"I... I think I could, if you'd give me a little time to get used to the system."

"I can give you 30 seconds."  
"How generous of you, Commander."

Shepard took Grunt from Thane's arms as the Drell set to work on the keys set around the large pillar. The Commander grabbed an adrenalin shot from his medical pouch and slammed it into the Krogan's neck, depressing the plunger.

"That oughta help for a little while. Hang in there big guy." Shepard spoke into the side of Grunt's head.

The large door through which the squad had entered was being rapidly breached by an army of mutated clones. The rivets holding the door together were flying out with every impact of their combined efforts, and it was at this point that Shepard had a plan.

"Commander, I don't mean to add more problems to your list, but what do we do about that door?" Thane said, never taking his eyes off the holographic keys before him.

"We let them in, of course." Thane stopped, but only for a second.

"I don't think I understand... is that an Earth expression?"

"No, it's a literal instruction. Let them in in exactly ten seconds. You can operate the door from there, surely."

"Well yes, but-"

"Good. Do it."

"Whatever you say, Shepard."

The Commander withdrew two disc grenades from his belt, and flung them at the long, thin path stretching from the door to the platform. The hit the polished surface but, mercifully, held tight and stuck. At the same time, blue lights on their domed surfaces began flashing urgently.

"Five seconds until door release, Commander."

"Get ready to move those mechanical arms, Thane. Then get ready to move your legs."

"Three seconds."

_This had better work, _Shepard thought to himself, _I swear this had better goddamn work..._"

"Two seconds."

Grunt groaned weakly as the adrenalin started to fade and his heart began to stop. His rich mandarin scales were turning paler before Shepard's eyes.

"One second, Shepard."

Shepard detonated the disc mines. Orange clouds of flame engulfed the path blowing a gap about ten feet wide between the curved surface of the wall and the path. The platform shuddered with the force of the impact, and began to tilt...

"Door opening, Shepard."

As expected, dozens of clones flooded through the door... and into the abyss. As each soldier followed a path that wasn't there, they fell gracelessly into the murky depths of the facility hundreds of feet below the platform, each screaming the last of their breath before vanishing out of sight.

"Thane, get one of those arms to stop underneath this platform."

"Underneath, Commander?"

"Underneath. Here meaning, slightly below where I am standing."

"As you wish..." Thane was far from used to the Commander's methods, but had seen enough near-misses and close-escapes to trust them.

With no support from the opposite side, the remaining path began to bend, tilting the platform more and more. Only the glass pillar held the heavy platform where it was now, and that too was beginning to strain.

"Arm's in place, Shepard."

"Good work, Thane. Now stand over here and help me slide this Krogan onto it."

"The platform continued to tilt, the once-flat surface becoming steeper and steeper until the squad began to slide down it. A large stretch of dark steel held on an arm awaited them at the bottom of the slope."

"Go, go! Get Grunt onto that arm!" Thane did as instructed, kicking the Krogan indelicately. Before long, they were both sliding quickly down the steel until...

_Thud._ Thane landed in a roll, stopping himself from going too far and flying off the arm; the unconscious Grunt simply slumped onto it, apparently unconcerned the whole affair.

Shepard lingered at the pillar, grasping the keys that Thane had been working. Holding himself up with one hand, he used the other to frantically hammer in a few words. He then hit a flashing icon labelled 'send', and slid down to meet his squad at the arm. Shepard dashed to a small emergency access panel at the far end of the arm and opened it. An array of tangled wires and one large button greeted him.

"Thane, can you hack this?" The Drell looked over his shoulder.

"...No, Commander."

"Then you'd better start praying to your Gods now – I'm hitting this button."

"Shepard, no! That could do anyth-!" The Drell was interrupted by a tremor shivering down the arm as Shepard punched the button and retreated to Grunt, securing him with one hand and himself with the other. Suddenly, the arm moved backwards in on itself and vertically upwards, darting away from the platform and pinning the squad to the floor. Beneath them, the little round platform forced cracks into the glass, which darted up the surface of the pillar like they themselves were trying to escape. Finally, the platform crashed through the glass pillar, and was immediately vaporised by the beam contained within. The light then arced frantically out of the pillar like lightning, destroying everything it touched with its forking tendrils as the squad's mechanical arm carried them into one of the tunnels.

Suddenly, the arm stopped, jolting the Drell and the human whilst the Krogan lay quite peacefully, almost dead.

"Dammit Grunt, stay with us!" Shepard slapped the Krogan as hard as he could, but to no end.

"Shepard, look!" Thane was indicating a narrow shaft of light, no more then three feet wide, slicing through the alarm-polluted red of the tunnel. This light came from a vent that led straight up and out, and was only a yard away from them down the tunnel. But how to get up there?

Shepard fired up a comm channel to the Normandy.

"Joker!"

"We're in position above the facility, Commander. Awaiting your orders. Where are you?"

"In a tunnel near the surface. Send down the shuttle – look for a vent or something."

"But you sai-"

"Don't even start, Lieutenant. Get someone on that shuttle, give them a rope, and tell them to find us.

"Commander, I can see your location on our thermals. I think they can get to you without too much trouble."

"Good. And do it on the double, or by the time you get in here we'll be no more than very pissed-off dust."

"I'm on it, Shepard."

The Commander cut the comms for the second time, and began dragging Grunt off the stationary arm towards the beam of light. Thane took the Krogan's other stubby arm and helped pull him. They arrived in the pool of light about a minute later, as a shadow crossed over it. The shuttle's engines cut out above them as a pair of feet thudded against the grassy surface and gunshots hit the vent.

"Get clear down there!" Yelled a Turian voice as more bullets hit the metal grill above them. A metal rope was dropped down. Thane and Shepard rapidly fastened the Krogan to it, then themselves, and were soon lifted up through the hole.

"Nice to see you, Commander." Shepard was greeted by the half-mutilated face of Garrus Vakarian, who proudly held his sniper rifle aloft.

"The pleasure's all mine. Now get this Kroagn on the shuttle and let's _leave._"

The crew hurried into the shuttle, which promptly returned to the Normandy's second incarnation as the facility was utterly destroyed in a blitzkrieg of white light.

Meanwhile, many systems away, Shepard's hurried message found its target.

"This just came in for you, General."

The General of the Blue Suns did not like to be disturbed - not one bit, and as he turned to the shy-looking Batarian who was extending a holopad out to him, he tried to restrain himself from shooting the rookie. Instead, he swiped the device from his hand and read the message.

"All your base are belong to us. Love, Shepard."

The General of the Blue Suns flew into a frenzied rage. The last thing the Batarian rookie saw was a very, _very _angry form flailing in hatred, and a sidearm drawn at his quivering face. The General did not restrain himself.


End file.
